Searching journal content for articles similar to Mezlini et al. 23 (3): 519.

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  1. Method: TransMeta simultaneously assembles multisample RNA-seq reads
    • Ting Yu,
    • Xiaoyu Zhao,
    • and Guojun Li
    Genome Res. July 2022 32: 1398-1407; Published in Advance July 20, 2022, doi:10.1101/gr.276434.121
    ...al. 2015), Cufflinks (Trapnell et al. 2010), Class2 (Song et al. 2016), Scripture (Guttman et al. 2010), IsoInfer (Feng et al. 2011), IsoLasso (Li et al. 2011), iReckon (Mezlini et al. 2013), CEM (Li and Jiang 2012), Traph (Tomescu et al. 2013), and MITIE (Behr et al. 2013) can be used to reconstruct...
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  2. Method: AIDE: annotation-assisted isoform discovery with high precision
    • Wei Vivian Li,
    • Shan Li,
    • Xin Tong,
    • Ling Deng,
    • Hubing Shi,
    • and Jingyi Jessica Li
    Genome Res. December 2019 29: 2056-2072; Published in Advance November 6, 2019, doi:10.1101/gr.251108.119
    ...should be added to improve the solution. Another method, iReckon, takes a different approach and tackles the isoform discovery problem via maximum likelihood estimation (Mezlini et al. 2013). It first constructs all the candidate isoforms supported by RNA-seq data, and then it uses a regularized...
  3. Method: TransBorrow: genome-guided transcriptome assembly by borrowing assemblies from different assemblers
    • Ting Yu,
    • Zengchao Mu,
    • Zhaoyuan Fang,
    • Xiaoping Liu,
    • Xin Gao,
    • and Juntao Liu
    Genome Res. August 2020 30: 1181-1190; Published in Advance August 17, 2020, doi:10.1101/gr.257766.119
    ..., Fiume M, Buske O, Savich GL, Shah S, Aparicio S, Chiang DY, Goldenberg A, Brudno M. 2013. iReckon: simultaneous isoform discovery and abundance estimation from RNA-seq data. Genome Res 23: 519–529. doi:10.1101/gr.142232.112 ↵Niknafs YS, Pandian B, Iyer HK, Chinnaiyan AM, Iyer MK. 2017. TACO produces...
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